X-71212113-A-C

Variant names:

• chrX-71212113-A-C
• rs7058793

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.37 (7386 hom., 9759 hem., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.369 AC: 38960 AN: 105472 Hom.: 7381 Cov.: 19

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.338

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.370 AC: 38981 AN: 105492 Hom.: 7386 Cov.: 19 AF XY: 0.340 AC XY: 9759 AN XY: 28670

African (AFR) AF: 0.700 AC: 19764 AN: 28235

American (AMR) AF: 0.435 AC: 4212 AN: 9691

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 645 AN: 2591

East Asian (EAS) AF: 0.298 AC: 994 AN: 3334

South Asian (SAS) AF: 0.252 AC: 611 AN: 2423

European-Finnish (FIN) AF: 0.155 AC: 813 AN: 5250

Middle Eastern (MID) AF: 0.293 AC: 60 AN: 205

European-Non Finnish (NFE) AF: 0.218 AC: 11267 AN: 51673

Other (OTH) AF: 0.337 AC: 481 AN: 1429

Alfa AF: 0.294 Hom.: 20965

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.65
DANN	Benign	0.42
PhyloP100		-0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7058793; hg19: chrX-70431963;